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Carbon-14 (C-14) has been widely used to estimate groundwater recharge rates in arid regions, and is increasingly being used as a tool to assist numerical model calibration. However, lack of knowledge on C-14 inputs to groundwater potentially limits its reliability for constraining spatial variability in recharge. In this study, we use direct measurements of C-14 in the unsaturated zone to develop a C-14 input map for a regional scale unconfined aquifer in the Ti Tree Basin in central Australia. The map is used as a boundary condition for a 3-D groundwater flow and solute transport model for the basin. The model is calibrated to both groundwater C-14 activity and groundwater level, and calibration is achieved by varying recharge rates in 18 hydrogeological zones. We test the sensitivity of the calibration to both the C-14 boundary condition, and the number or recharge zones used. The calibrated recharge rates help resolve the conceptual model for the basin, and demonstrate that spatially distributed discharge (through evapotranspiration) is an important part of the water balance. This approach demonstrates the importance of boundary conditions for C-14 transport modeling (C-14 input activity), for improving estimates of spatial variability in recharge and discharge.